DESCRIPTION

Bio::Tools::SeqStats is a lightweight object for the calculation of simple statistical and numerical properties of a sequence. By "lightweight" I mean that only "primary" sequences are handled by the object. The calling script needs to create the appropriate primary sequence to be passed to SeqStats if statistics on a sequence feature are required. Similarly if a codon count is desired for a frame-shifted sequence and/or a negative strand sequence, the calling script needs to create that sequence and pass it to the SeqStats object.

Nota that nucleotide sequences in bioperl do not strictly separate RNA and DNA sequences. By convention, sequences from RNA molecules are shown as is they were DNA. Objects are supposed to make the distinction when needed. This class is one of the few where this distinctions needs to be made. Internally, it changes all Ts into Us before weight and monomer count.

SeqStats can be called in two distinct manners. If only a single computation is required on a given sequence object, the method can be called easily using the SeqStats object directly:

$weight = Bio::Tools::SeqStats->get_mol_wt($seqobj);

Alternately, if several computations will be required on a given sequence object, an "instance" statistics object can be constructed and used for the method calls:

As currently implemented the object can return the following values from a sequence:

The molecular weight of the sequence: get_mol_wt()

The number of each type of monomer present: count_monomers()

The number of each codon present in a nucleic acid sequence: count_codons()

The mean hydropathicity ("gravy" score) of a protein: hydropathicity()

For DNA and RNA sequences single-stranded weights are returned. The molecular weights are calculated for neutral, or not ionized, nucleic acids. The returned weight is the sum of the base-sugar-phosphate residues of the chain plus one weight of water to to account for the additional OH on the phosphate of the 5' residue and the additional H on the sugar ring of the 3' residue. Note that this leads to a difference of 18 in calculated molecular weights compared to some other available programs (e.g. Informax VectorNTI).

Note that since sequences may contain ambiguous monomers (e.g. "M", meaning "A" or "C" in a nucleic acid sequence), the method get_mol_wt returns a two-element array containing the greatest lower bound and least upper bound of the molecule. For a sequence with no ambiguous monomers, the two elements of the returned array will be equal. The method count_codons() handles ambiguous bases by simply counting all ambiguous codons together and issuing a warning to that effect.

DEVELOPERS NOTES

Ewan moved it from Bio::SeqStats to Bio::Tools::SeqStats

Heikki made tiny adjustments (+/- 0.01 daltons) to amino acid molecular weights to have the output match values in SWISS-PROT.

Torsten added hydropathicity calculation.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Peter Schattner

Email schattner AT alum.mit.edu

CONTRIBUTOR - Torsten Seemann

Email torsten.seemann AT infotech.monash.edu.au

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

count_monomers

Title : count_monomers
Usage : $rcount = $seq_stats->count_monomers();
or $rcount = $seq_stats->Bio::Tools::SeqStats->($seqobj);
Function: Counts the number of each type of monomer (amino acid or
base) in the sequence.
Ts are counted as Us in RNA sequences.
Example :
Returns : Reference to a hash in which keys are letters of the
genetic alphabet used and values are number of occurrences
of the letter in the sequence.
Args : None or reference to sequence object
Throws : Throws an exception if type of sequence is unknown (ie amino
or nucleic)or if unknown letter in alphabet. Ambiguous
elements are allowed.

get_mol_wt

Title : get_mol_wt
Usage : $wt = $seqobj->get_mol_wt() or
$wt = Bio::Tools::SeqStats ->get_mol_wt($seqobj);
Function: Calculate molecular weight of sequence
Ts are counted as Us in RNA sequences.
Example :
Returns : Reference to two element array containing lower and upper
bounds of molecule molecular weight. For DNA and RNA
sequences single-stranded weights are returned. If
sequence contains no ambiguous elements, both entries in
array are equal to molecular weight of molecule.
Args : None or reference to sequence object
Throws : Exception if type of sequence is unknown (ie not amino or
nucleic) or if unknown letter in alphabet. Ambiguous
elements are allowed.

count_codons

Title : count_codons
Usage : $rcount = $seqstats->count_codons() or
$rcount = Bio::Tools::SeqStats->count_codons($seqobj)
Function: Counts the number of each type of codons for a dna or rna
sequence, starting at the 1st triple of the input sequence.
Example :
Returns : Reference to a hash in which keys are codons of the genetic
alphabet used and values are number of occurrences of the
codons in the sequence. All codons with "ambiguous" bases
are counted together.
Args : None or sequence object
Throws : an exception if type of sequence is unknown or protein.

_is_alphabet_strict

Title : _is_alphabet_strict
Usage :
Function: internal function to determine whether there are
any ambiguous elements in the current sequence
Example :
Returns : 1 if strict alphabet is being used,
0 if ambiguous elements are present
Args :
Throws : an exception if type of sequence is unknown (ie amino or
nucleic) or if unknown letter in alphabet. Ambiguous
monomers are allowed.